Antibiotics are designed to stamp out the microbes that make us sick, but their overuse has resulted in drug-resistant bacteria. These "superbugs" have modified their behavior to defy even the best medical efforts and are a growing public health concern. Recently published in the journal Nature, a paper by researchers from Northeastern University, Pacific Northwest National Laboratory, and Arietis Biotechnology describes how these superbugs could be prompted to self-destruct.
With an eye toward maximizing isoprene production in bacteria, a team of PNNL and EMSL staff and users developed a new transcriptomics-based model that accurately predicts how much isoprene the bacterium Bacillus subtilis will produce when stressed or nourished. This model marks a step toward understanding how changes in the bacteria's environment affect gene expression and, in turn, isoprene production. Isoprene is a volatile liquid currently derived from oil that is used for aviation fuel and industrial applications.
Scientists at PNNL looking to create a potent blend of enzymes to transform materials like corn stalks and wood chips into fuels have developed a test that should turbocharge their efforts. Using a PNNL-developed chemical probe, part of an activity-based protein profiling system, on the fungus Trichoderma reesei, they tracked precisely how each of dozens of the fungus's enzymes reacts to changing conditions. Their findings open the possibility that laboratory research now taking months could be reduced to days, and that scientists will be able to assess more options for biofuel development than is possible today.
Scientists can now recover and identify twice as many proteins expressed by soil-dwelling microbes than they could previously thanks to a new method of soil pretreatment developed by a scientific team led by Pacific Northwest National Laboratory researchers. The strategy for processing samples reveals new insight into the function of microbial communities in their native environments. Such insight helps to define the communities' fundamental biogeochemical roles in carbon cycling, nitrogen cycling, phosphorus cycling, and climate regulation. It also helps to determine how these communities might assist with environmental cleanup.
The central dogma of biology is that DNA gives rise to mRNA, which then gives rise to protein. Thus, it has been widely assumed that changes in specific mRNA levels are always accompanied by commensurate changes in the encoded proteins. To determine whether this is always the case, PNNL scientists examined Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Surprisingly, they found that changes in protein expression in response to altered oxygen levels were caused primarily by differences in the translational efficiency of the mRNAs rather than changes in the mRNA levels. Their data suggest that changes in the translational efficiency of proteins and protein levels are caused partly by alterations in the translational machinery and associated molecules. The work provides a foundation for more detailed mechanistic studies to understand how cells control protein expression and explore why translational efficiency changes under different cell environments.